General Discussion - BioGearshttps://biogearsengine.com/forums/categories/general/feed.rss
Fri, 22 Feb 2019 14:13:57 +0000General Discussion - BioGearsen-CAQuestion about BioGears and immune responsehttps://biogearsengine.com/forums/discussion/71/question-about-biogears-and-immune-response
Thu, 09 Nov 2017 08:13:55 +0000JPLeRouzic71@/forums/discussionsThanks for providing us this fantastic tool.I am thinking about how to use BioGears for quickly asserting if a peptide vaccine is dangerous or not. At least it could be interested to know if the injected peptide is eliminated quickly from the body (PD/PK scenario). But who knows it might provide more insights (is it poisonous, influence on physiological systems, on metabolism).Indeed I am aware that BioGears is not designed for this kind of extensive scenario, but as far I know there are no public resources that makes it possible to evaluate the effects of a peptide on health, so even a rough result would be a significant progress for me.

I'm working on a project where i'm developing a web app, which later I would connect with your engine to get more accurate results.

BioGears would have to be running on a AWS Instance, which then I would have to connect with my Web app.

Though, I've been reading and searching around, and I can't find a way to do that connection. Not an API or anything like that

Any clue of how can I do it?

Thanks]]>Stochastic signal generationhttps://biogearsengine.com/forums/discussion/40/stochastic-signal-generation
Tue, 18 Jul 2017 15:47:45 +0000bfegley40@/forums/discussionsCan one introduce randomness (variance) in the generation of DataRequests (metrics of interest)? If so, how might that be accomplished without the use of Actions, via the toolkit (underlying XML) or programmatically via the SDK? For context, from some simple tests of mine, signals for heart rate and respiration rate do not change in the output (regardless of sampling rate) unless an Action (other than advancing time or serializing state) is introduced. Guidance appreciated.

Thanks much, Brent

(BioGears is awesome! Keep up the great work!)]]>Changing the Engine Parameter Grouphttps://biogearsengine.com/forums/discussion/44/changing-the-engine-parameter-group
Thu, 10 Aug 2017 08:08:02 +0000evolve3444@/forums/discussionsAdvance sorry for my English, I hope that you will understand my questions.

We want to change the following group of engine parameters: heart rate, respiration rate (RR), SpO2 (concentration of oxyhemoglobin in arterial blood), but there must be a correlation between these parameters, i.e. If we change the heart rate, then the respiration rate should also give a reaction. The heart rate is almost adequately controlled, but the respiration rate does not respond to our manipulations. We want the patient's RR to rise from 16 to 30 and stay at that level. Tried to include the following compartments of the respiratory system and to change the pressure and resistance values in the nodes and paths: Ambient, Mouth, Carina, Left (Right) Dead Space, Left (Right) Alveoli + from the cardiovascular system included the following: Right (Left) Pulmonary Arteries, Capillaries , Veins.But the engine for a short time catches events such as respiratory alkalosis, hypoxia and quickly out of them. What else have we not considered? Through which nodes can adequately control the concentrations of O2 and CO2? We tried various combinations of electrical schemes of cardiovascular and respiratory systems, but did not get the desired result. Can still some need to include compartments and systems in the work of the engine?

I hope for help in this exciting issue.]]>Sourcing informationhttps://biogearsengine.com/forums/discussion/38/sourcing-information
Mon, 22 May 2017 15:09:57 +0000Fpuente_AFMMAST38@/forums/discussionsI am in the Government sector (Air Force Medical Modeling Simulation & Training). I wanted to see if anyone knew of other entities specifically vendors that offered similar capabilities to what Biogears provides? We are working on gearing up our portfolio in the medical modeling space. Any information on other companies providing this type of service is much appreciated!]]>CDM Tableshttps://biogearsengine.com/forums/discussion/37/cdm-tables
Sun, 09 Apr 2017 10:06:20 +0000EdVcom3D37@/forums/discussionsSystem specificcations to run Biogears enginehttps://biogearsengine.com/forums/discussion/30/system-specificcations-to-run-biogears-engine
Tue, 11 Oct 2016 16:57:56 +0000PavithraBME30@/forums/discussionsWould like to know if there is any recommended system specifications for a laptop to run Biogears engine. We want to reduce the initialization time and run-time for running different scenarios.

Thanks,Pavi ]]>Respiration Cyclehttps://biogearsengine.com/forums/discussion/29/respiration-cycle
Sun, 09 Oct 2016 09:32:31 +0000avivshamsian29@/forums/discussionsI perform a Respiration Cycle experiment and i would like to control few parameters :1) Where can I define the FRC values? I have tried in the patient files.2) How can I determine measuring points in the model?

Thanks for the helpers!Have a good day.]]>GUI display issues in windows 10https://biogearsengine.com/forums/discussion/32/gui-display-issues-in-windows-10
Tue, 06 Dec 2016 20:21:48 +0000PavithraBME32@/forums/discussionsIssue with Java JRE "Can't Find Dependent Libraries"https://biogearsengine.com/forums/discussion/31/issue-with-java-jre-can-t-find-dependent-libraries
Mon, 05 Dec 2016 15:29:18 +0000noel17031@/forums/discussionsI am having an issue getting the BioGears toolkit to run properly on my computer. My computer is running Windows 10 on a 64-bit OS. I've downloaded the proper Java JRE update and have the JAVA_HOME and Path variables pointing to the right directories on my system; however, whenever I download the toolkit and attempt to run the CombatMultiTrauma scenario, I encounter this error within the log files:

I've tried loading other scenarios as well, and some of them will load properly, but I encounter the same issue when I attempt to execute the scenario. I'm not familiar with Java, so I'm having a bit of difficulty determining the root cause of the problem, but any help on this issue would be greatly appreciated. Thank you!]]>CPMS Webinarhttps://biogearsengine.com/forums/discussion/28/cpms-webinar
Wed, 07 Sep 2016 17:11:50 +0000rmetoyer28@/forums/discussionsThank you all,Rodney Metoyerrmetoyer@ara.com]]>PhD position for physiologically based medical simulationhttps://biogearsengine.com/forums/discussion/27/phd-position-for-physiologically-based-medical-simulation
Mon, 06 Jun 2016 18:50:14 +0000MichelODU27@/forums/discussionsCandidates should enquire with Prof. Jim Leathrum of Old Dominion University by email: jleathru@odu.edu. ]]>Java stopped workinghttps://biogearsengine.com/forums/discussion/26/java-stopped-working
Mon, 18 Apr 2016 08:40:30 +0000Asher_Kuper26@/forums/discussionsI get a message: "Java(TM) Platform SE binary has stopped working"I restarted my PC and install the latest Java update (Java 8 update 77).What else can I do?Thanks,Asher]]>Help getting startedhttps://biogearsengine.com/forums/discussion/23/help-getting-started
Wed, 06 Jan 2016 22:17:42 +0000kyleh1103023@/forums/discussionsThanks,Kyle]]>Getting Startedhttps://biogearsengine.com/forums/discussion/24/getting-started
Mon, 21 Mar 2016 17:47:26 +0000rthechief24@/forums/discussionsOther info:

I've tried running the .bat BioGearsGUI file from WINE, but that has similar issues to another thread I read on here, where a terminal will pop up then my current terminal spits out an error message and the GUI doesn't even pop up.

I am currently using the BioGearsTK.

Thanks for looking into this!]]>autonomic nervous system controlhttps://biogearsengine.com/forums/discussion/22/autonomic-nervous-system-control
Tue, 05 Jan 2016 18:49:52 +0000Hal22@/forums/discussionsI understand that the cardiovascular model uses a variable compliance model ( C ~ 1/P ?) but was wondering if there was heart rate and compliance control as determined by sympathetic and parasympathetic control (using actual relative time delays, response functions and sensitivities). If not, is this deemed more fine turning than necessary for gross injury modeling ?]]>Different cardiovascular models for different clinical problems with different time-scaleshttps://biogearsengine.com/forums/discussion/7/different-cardiovascular-models-for-different-clinical-problems-with-different-time-scales
Tue, 24 Feb 2015 00:41:19 +0000acorbett7@/forums/discussionsRight now Biogears is " running anywhere between real time (1 second real time to simulate 1 second of our patient/scenario) to 5x real time (10 seconds of real time to simulate 50 seconds of our patient/scenario)" (Per Abray from another discussion)

I suggest that this is too slow to support many desired applications of Biogears for simulation-based learning. In my own work, I have simulated from a minute/sec up to an hour/sec depending on the clinical problem and it's natural time course. And indeed, Abray confirmed that they are working on optimizing the code, and also making it possible to swap out sub-models of differing complexity/resolution. The following describes a specific suggestion along the lines...

I would guess that the major reason for the current performance is the computational demand of simulating the cardiovascular system at a fine temporal scale. Clearly the temporal scale has to be very fine in order to simulate individual beats and ECG patterns, as you appear to be doing. Therefore the time slices (dt) are very small and the calculations intensive, and so it naturally takes a long time to simulate -- accounting for the current ratio of simulated:real time. Of course, if the Biogears folks tell me I'm mistaken in this assumption then you can ignore the rest of this and I'll just quote Rosanne Rosanadana and say "Never mind." ;-)

This fine-grained simulation of the cardiovascular system obviously makes good sense for training around acute trauma or cardiovascular insults, where the temporal details matter a lot and decision making has to occur on the scale of seconds-to-minutes. However, there are many clinical problems where this high resolution of cardiovascular function is not needed, and becomes a barrier to building effective learning simulations. This would include any clinical problem that evolves over hours -to-days such as poisoning, pain management, diabetes crises, kidney failure, etc.

With this in mind, I propose that you create an explicit, low-resolution cardiovascular model to use for these types of cases. One typical approach is to treat the cardiovascular system as a closed fluid flow system (with pump & compartments) in which heart rate and blood pressure respond to changes in volume and resistance at various points in the circuit (and vice versa), but only at a gross level -- you can predict current heart rate (and other system variables) but you can't represent individual beats (not mathematically anyway). One example of this approach can be found in Chapter 5 of Hoppensteadt & Peskin's "Mathematics in Medicine and Life Sciences", Springer, 1992. I've actually implemented this as a simple systems model.

I suspect that this one enhancement -- having two cardio models at 2 different resolutions, and providing a toggle to choose betwen them -- would relieve a lot of the computational load for clinical scenarios that don't require fine-grained modeling of heart function. I can't think of another physiological process that would even require the same fine temporal resolution as cardio function does.

I'd love to hear other thoughts on this...

andrew]]>Biogears as a server-side engine for browser-based medical training simulations?https://biogearsengine.com/forums/discussion/6/biogears-as-a-server-side-engine-for-browser-based-medical-training-simulations
Sun, 22 Feb 2015 23:00:38 +0000acorbett6@/forums/discussionsFirst of all, I absolutely love the concept and goal of Biogears. One of the big challenges in developing training simulations is having the virtual patient dynamically respond to the injury and interventions in a clinically realistic way. This requires valid mathematical simulations to drive things behind the scenes -- but not everyone has the time, resources, or expertise to develop such simulations. Nor should everyone be "re-inventing the wheel". Enter Biogears ... and I find that to be totally awesome ;-)

I've downloaded the toolkit and SDK and have started exploring. I've posted to a couple other discussions some issues I've run into, which others have too. My particular interest is investigating whether I can wrap Biogears in some .net (C#) code so as to make it a server-side engine for browser-based training sims. The front end for said sims could be HTML5/Canvas -- e.g., using EaselJS -- or it could be Unity3D exported as HTML5. (Or Flash, of course, but no need to elaborate on that...).

Along these lines, I have some questions for the Biogears team (or for others who may be exploring similar concepts):1) To what extent is this an explicit goal for Biogears? Have you investigated this possibility internally? Or have you possibly already decided it is not a feasible objective?2) Clearly the current implementation does not perform well enough to serve as such an engine. Here I'm referring to the current slow speed of execution which has been noted and confirmed elsewhere. I understand there are plans to optimize the code and improve performance. Is it an objective to have it run fast enough to realistically provide a flight-sim like capability?3) Related to the above, it seems that part of the optimization may involve NOT having a single, comprehensive, mechanistically-accurate physiological simulation that serves all needs. Perhaps you are considering making it so only the minimally required simulation "modules" are loaded and used? Or perhaps creating a simpler (swappable?) components that are more phenomenological in nature and therefore less computationally intensive?

I'd love to hear any answers/thoughts on these questions that you are willing and able to share. In the meantime I'm going to poke around with creating a .net implementation if only as a crude proof-of-concept.